Phase partitioning of NHx (gaseous NH3 and particulate NH4+) in the atmosphere is crucial for the lifetime of NHx during atmospheric transport. Reliable data for gaseous NH3 and NH4+ in aerosols are necessary to understand phase-partitioning and atmospheric cycles of NHx. A semi-continuous microflow analytical system (MF system) was developed for measuring gaseous NH3 and particulate NH4+ in the atmosphere. Two inlet lines were used to differentiate total amounts of NHx and particulate NH4+ after gaseous NH3 were removed by phosphoric acid coated denuder from the sample air stream. Small water droplets were mixed with sample air and separated for liquid phase analysis in the MF system. The NH4+ concentration in the liquid was measured using sensitive fluorescence detection after reaction with o-phthalaldehyde and sulfite. Based on air sampling at a flow rate of 1 L/min with stripping water at a flow rate of 100 μL/min, the MF system can analyze down to 3 nmol/m3 of atmospheric NH3 concentration at 15 min intervals. Comparison with data based on the annular denuder method for gaseous NH3 and particulate NH4+ concentrations indicated reasonable agreement with the MF system. Field tests of the MF system for one month showed good agreement with NH4+ concentrations of fine particles collected daily on PTFE filters at the site. The MF system can monitor gaseous NH3 and particulate NH4+ concentrations at 30 min intervals, thereby providing short-term phase partitioning data of NHx.